Plotting

Plotting the data produced is all contained in the postprocessing module and specifically the --column flag or PlotColumns in your input file. When plotting data, a new data file will be written containing all the data that could be plotted. There are three files that can be written; an extended xyz file, a momenta file and an energy file. The program does not read any data from this file, all manipulation of the data is done internally:

To plot two sets of data against each other, for example, time and total energy.

--column time Etotal

The above will only work for a single statistical run. If the calculation was run with more than one statistical run you will need to specify the run you want to plot such as:

--column time "Etotal[0, :]"

This can be extended to plot multiple sets at once. The below example also shows how to split a matrix into a desired shape. The addition of quotes is required to stop bash interfering with the input.

--column time Etotal time "Mtotal[:, 0]"

You can also do basic arithmetic on the data sets such as:

--column time mag_pot+trans_pot

Possible variables

Matrix Dimensions Key - S = Statistical Runs I = Iterations, N = Number of molecules, C = XYZ Coordinates (3)

XYZ data - S*I*N*C

position
magnetisation
forces
momentum

Energy data - S*I

Etotal
mag_pot
trans_pot
kinetic

Momenta data - S*I*C

Mtotal
total_mag
total_angular
CoM
CoM_mom

Other

time - I